Introduction
In this tutorial we learn how to install idba
on Ubuntu 20.04.
What is idba
idba is:
IDBA stands for iterative de Bruijn graph assembler. In computational
sequence biology, an assembler solves the puzzle coming from large
sequencing machines that feature many gigabytes of short reads from a
large genome.
This package provides several flavours of the IDBA assembler, as they all
share the same source tree but serve different purposes and evolved over time.
IDBA is the basic iterative de Bruijn graph assembler for
second-generation sequencing reads. IDBA-UD, an extension of IDBA,
is designed to utilize paired-end reads to assemble low-depth regions
and use progressive depth on contigs to reduce errors in high-depth
regions. It is a generic purpose assembler and especially good for
single-cell and metagenomic sequencing data. IDBA-Hybrid is another
update version of IDBA-UD, which can make use of a similar reference
genome to improve assembly result. IDBA-Tran is an iterative de Bruijn
graph assembler for RNA-Seq data.
There are three methods to install idba
on Ubuntu 20.04. We can use apt-get
, apt
and aptitude
. In the following sections we will describe each method. You can choose one of them.
Install idba Using apt-get
Update apt database with apt-get
using the following command.
sudo apt-get update
After updating apt database, We can install idba
using apt-get
by running the following command:
sudo apt-get -y install idba
Install idba Using apt
Update apt database with apt
using the following command.
sudo apt update
After updating apt database, We can install idba
using apt
by running the following command:
sudo apt -y install idba
Install idba Using aptitude
If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Ubuntu. Update apt database with aptitude
using the following command.
sudo aptitude update
After updating apt database, We can install idba
using aptitude
by running the following command:
sudo aptitude -y install idba
How To Uninstall idba on Ubuntu 20.04
To uninstall only the idba
package we can use the following command:
sudo apt-get remove idba
Uninstall idba And Its Dependencies
To uninstall idba
and its dependencies that are no longer needed by Ubuntu 20.04, we can use the command below:
sudo apt-get -y autoremove idba
Remove idba Configurations and Data
To remove idba
configuration and data from Ubuntu 20.04 we can use the following command:
sudo apt-get -y purge idba
Remove idba configuration, data, and all of its dependencies
We can use the following command to remove idba
configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge idba
References
Summary
In this tutorial we learn how to install idba
package on Ubuntu 20.04 using different package management tools: apt
, apt-get
and aptitude
.